Estimate expression data from SRA run and reference genome

Source: R/estimate_expression.R

Example

estimate_expression(
  run_accession,
  sra_fname,
  is_paired,
  results_dir,
  logs_dir,
  work_dir,
  reference_genome_path,
  fastq_dump_program,
  rsem_calculate_expression_program,
  bowtie2_path,
  n_threads = 1
)

Arguments

run_accession

identifier for exprsesion run
sra_fname

path to .sra file for the run
is_paired

is it paired end read expression data?
results_dir

path where the results should be stored
logs_dir

path where the logs should be stored
work_dir

path where intermediate data should be stored
reference_genome_path

path to reference genome
fastq_dump_program

path to fastq_dump
rsem_calculate_expression_program

path to rsem-calculate-expression

Details

tag <- "20201209" estimate_expression( run_accession = "SRR513613", sra_fname = "/scratch/maom_root/maom99/maom/CryptoCEN/sra/SRR513613/SRR513613.sra", is_paired = TRUE, results_dir = "intermediate_data/estimated_expression_20201209", results_dir = "intermediate_data/estimated_expression_20201209/logs", work_dir = "/scratch/maom_root/maom99/maom/CryptoCEN/estimated_expression_20201209", reference_genome_path = "/scratch/maom_root/maom99/maom/CryptoCEN/reference_geneome", fastq_dump_program = "